libSBML Python API
5.10.0
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{comp}
comp Implementation of the ExternalModelDefinition construct from the “comp” package.The ExternalModelDefinition class was introduced by the SBML Level 3 Hierarchical Model Composition package (“comp”) to define references to Model objects defined in other files.
ExternalModelDefinition objects are model definitions—in and of themselves, they are definitions of models but not uses of those models. The class provides a way to declare and identify them so that Model objects in the present SBML document can use them in Submodel objects.
ExternalModelDefinition contains two required attributes ('source' and 'id') and three optional attributes ('modelRef', 'md5' and 'name').
The 'id' attribute serves to provide a handle for the external model reference so that Submodel objects can refer to it. Crucially, it is not the identifier of the model being referenced; rather, it is an identifier for this ExternalModelDefinition object within the current SBML document. The 'id' attribute takes a required value of type SId, and must be unique across all Model and ExternalModelDefinition objects present in the document.
ExternalModelDefinition also has an optional 'name' attribute, of type 'string'. The 'name' attribute may be used to provide a human-readable description of the ExternalModelDefintion object.
The required attribute 'source' is used to locate the SBML document containing an external model definition. The value of this attribute must be of type anyURI. Since URIs may be either URLs, URNs, or relative or absolute file locations, this offers flexibility in referencing SBML documents. In all cases, the 'source' attribute value must refer specifically to an SBML Level 3 Version 1 document; prior Levels/Versions of SBML are not supported by this package. The entire file at the given location is referenced. The 'source' attribute must have a value for every ExternalModelDefinition instance.
ExternalModelDefinition's optional attribute 'modelRef', of type SIdRef, is used to identify a Model or ExternalModelDefinition object within the SBML document located at 'source'. The object referenced may be the main model in the document, or it may be a model definition contained in the SBML document's ListOfModelDefinitions or ListOfExternalModelDefinitions lists. Loops are not allowed: it must be possible to follow a chain of ExternalModelDefinition objects to its end in a Model object.
In core SBML, the 'id' on Model is an optional attribute, and therefore, it is possible that the Model object in a given SBML document does not have an identifier. In that case, there is no value to give to the 'modelRef' attribute in ExternalModelDefinition. If 'modelRef' does not have a value, then the main model (i.e., the <model>
element within the <sbml>
element) in the referenced file is interpreted as being the model referenced by this ExternalModelDefinition instance.
Finally, the optional 'md5' attribute takes a string value. If set, it must be an MD5 checksum value computed over the document referenced by 'source'. This checksum can serve as a data integrity check over the contents of the 'source'. Applications may use this to verify that the contents have not changed since the time that the ExternalModelDefinition reference was constructed.
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Python method signature(s):
addCVTerm(SBase self, CVTerm term, bool newBag=False)int addCVTerm(SBase self, CVTerm term)
int
Adds a copy of the given CVTerm object to this SBML object.
term | the CVTerm to assign. |
newBag | if True , creates a new RDF bag with the same identifier as a previous bag, and if False , adds the term to an existing RDF bag with the same type of qualifier as the term being added. |
create
) for alternatives that do not lead to these issues.
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Python method signature(s):
appendAnnotation(SBase self, XMLNode annotation)int appendAnnotation(SBase self, string annotation)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
appendAnnotation(XMLNode annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object |
appendAnnotation(string annotation)
Appends the given annotation
to the 'annotation' subelement of this object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.
annotation | an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object |
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Python method signature(s):
appendNotes(SBase self, XMLNode notes)int appendNotes(SBase self, string notes)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
appendNotes(string notes)
Appends the given notes
to the 'notes' subelement of this object.
The content of the parameter notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML string that is to appended to the content of the 'notes' subelement of this object |
appendNotes(XMLNode notes)
Appends the given notes
to the 'notes' subelement of this object.
The content of notes
is copied.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML node structure that is to appended to the content of the 'notes' subelement of this object |
def libsbml.ExternalModelDefinition.clone | ( | self | ) |
{comp}
comp Implementation of the ExternalModelDefinition construct from the “comp” package.The ExternalModelDefinition class was introduced by the SBML Level 3 Hierarchical Model Composition package (“comp”) to define references to Model objects defined in other files.
ExternalModelDefinition objects are model definitions—in and of themselves, they are definitions of models but not uses of those models. The class provides a way to declare and identify them so that Model objects in the present SBML document can use them in Submodel objects.
ExternalModelDefinition contains two required attributes ('source' and 'id') and three optional attributes ('modelRef', 'md5' and 'name').
The 'id' attribute serves to provide a handle for the external model reference so that Submodel objects can refer to it. Crucially, it is not the identifier of the model being referenced; rather, it is an identifier for this ExternalModelDefinition object within the current SBML document. The 'id' attribute takes a required value of type SId, and must be unique across all Model and ExternalModelDefinition objects present in the document.
ExternalModelDefinition also has an optional 'name' attribute, of type 'string'. The 'name' attribute may be used to provide a human-readable description of the ExternalModelDefintion object.
The required attribute 'source' is used to locate the SBML document containing an external model definition. The value of this attribute must be of type anyURI. Since URIs may be either URLs, URNs, or relative or absolute file locations, this offers flexibility in referencing SBML documents. In all cases, the 'source' attribute value must refer specifically to an SBML Level 3 Version 1 document; prior Levels/Versions of SBML are not supported by this package. The entire file at the given location is referenced. The 'source' attribute must have a value for every ExternalModelDefinition instance.
ExternalModelDefinition's optional attribute 'modelRef', of type SIdRef, is used to identify a Model or ExternalModelDefinition object within the SBML document located at 'source'. The object referenced may be the main model in the document, or it may be a model definition contained in the SBML document's ListOfModelDefinitions or ListOfExternalModelDefinitions lists. Loops are not allowed: it must be possible to follow a chain of ExternalModelDefinition objects to its end in a Model object.
In core SBML, the 'id' on Model is an optional attribute, and therefore, it is possible that the Model object in a given SBML document does not have an identifier. In that case, there is no value to give to the 'modelRef' attribute in ExternalModelDefinition. If 'modelRef' does not have a value, then the main model (i.e., the <model>
element within the <sbml>
element) in the referenced file is interpreted as being the model referenced by this ExternalModelDefinition instance.
Finally, the optional 'md5' attribute takes a string value. If set, it must be an MD5 checksum value computed over the document referenced by 'source'. This checksum can serve as a data integrity check over the contents of the 'source'. Applications may use this to verify that the contents have not changed since the time that the ExternalModelDefinition reference was constructed. Python method signature(s):
clone(ExternalModelDefinition self)ExternalModelDefinition
Creates and returns a deep copy of this ExternalModelDefinition object.
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Python method signature(s):
disablePackage(SBase self, string pkgURI, string pkgPrefix)int
Disables the given SBML Level 3 package on this object.
This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.
An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from another SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:
import sys import os.path from libsbml import * # We read in an SBML L3V1 model that uses the 'comp' package namespace doc = readSBML('sbml-file-with-comp-elements.xml'); # We extract one of the species from the model we just read in. s1 = doc.getModel().getSpecies(0); # We construct a new model. This model does not use the 'comp' package. newDoc = SBMLDocument(3, 1); newModel = newDoc.createModel(); # The following would fail with an error, because addSpecies() would # first check that the parent of the given object has namespaces # declared, and will discover that s1 does but newModel does not. # newModel.addSpecies(s1); # However, if we disable the 'comp' package on s1, then the call # to addSpecies will work. s1.disablePackage('http://www.sbml.org/sbml/level3/version1/comp/version1', 'comp'); newModel.addSpecies(s1);
pkgURI | the URI of the package |
pkgPrefix | the XML prefix of the package |
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Python method signature(s):
enablePackage(SBase self, string pkgURI, string pkgPrefix, bool flag)int
Enables or disables the given SBML Level 3 package on this object.
This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().
pkgURI | the URI of the package. |
pkgPrefix | the XML prefix of the package |
flag | whether to enable (True ) or disable (False ) the package |
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Python method signature(s):
getAncestorOfType(SBase self, int type, string pkgName="core")SBase getAncestorOfType(SBase self, int type)
SBase getAncestorOfType(SBase self, int type, string pkgName="core")
SBase getAncestorOfType(SBase self, int type)
SBase
Returns the first ancestor object that has the given SBML type code from the given package.
LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_
.
This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName
.
type | the SBML type code of the object sought |
pkgName | (optional) the short name of an SBML Level 3 package to which the sought-after object must belong |
None
if no ancestor exists.pkgName
must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
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Python method signature(s):
getAnnotation(SBase self)XMLNode getAnnotation(SBase self)
XMLNode
Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.
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Python method signature(s):
getAnnotationString(SBase self)string getAnnotationString(SBase self)
string
Returns the content of the 'annotation' subelement of this object as a character string.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.
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Python method signature(s):
getColumn(SBase self)long
Returns the column number on which this object first appears in the XML representation of the SBML document.
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Python method signature(s):
getCVTerms()CVTermList
Get the CVTermList of CVTerm objects in this SBase.
Returns the CVTermList for this SBase.
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Python method signature(s):
getElementByMetaId(SBase self, string metaid)SBase
Returns the first child element it can find with a specific 'metaid' attribute value, or None
if no such object is found.
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.metaid | string representing the 'metaid' attribute value of the object to find. |
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Python method signature(s):
getElementBySId(SBase self, string id)SBase
Returns the first child element found that has the given id
in the model-wide SId
namespace, or None
if no such object is found.
id | string representing the 'id' attribute value of the object to find. |
def libsbml.ExternalModelDefinition.getElementName | ( | self | ) |
Python method signature(s):
getElementName(ExternalModelDefinition self)string
Returns the XML element name of this SBML object.
def libsbml.ExternalModelDefinition.getId | ( | self | ) |
Python method signature(s):
getId(ExternalModelDefinition self)string
Returns the value of the 'id' attribute of this ExternalModelDefinition.
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Python method signature(s):
getLevel(SBase self)long
Returns the SBML Level of the SBMLDocument object containing this object.
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Python method signature(s):
getLine(SBase self)long
Returns the line number on which this object first appears in the XML representation of the SBML document.
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Python method signature(s):
getListOfAllElementsFromPlugins(SBase self, ElementFilter filter=None)SBaseList getListOfAllElementsFromPlugins(SBase self)
SBaseList
Returns an SBaseList of all child SBase objects contained in SBML package plugins.
This method walks down the list of all packages used by the model and returns all objects contained in them.
def libsbml.ExternalModelDefinition.getMd5 | ( | self | ) |
Python method signature(s):
getMd5(ExternalModelDefinition self)string
Returns the value of the 'md5' attribute of this ExternalModelDefinition.
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Python method signature(s):
getMetaId(SBase self)string
Returns the value of the 'metaid' attribute of this object.
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
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Python method signature(s):
getModelHistory(SBase self)ModelHistory getModelHistory(SBase self)
ModelHistory
Returns the ModelHistory object, if any, attached to this object.
None
if none exist.def libsbml.ExternalModelDefinition.getModelRef | ( | self | ) |
Python method signature(s):
getModelRef(ExternalModelDefinition self)string
Returns the value of the 'modelRef' attribute of this ExternalModelDefinition.
def libsbml.ExternalModelDefinition.getName | ( | self | ) |
Python method signature(s):
getName(ExternalModelDefinition self)string
Returns the value of the 'name' attribute of this ExternalModelDefinition.
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Python method signature(s):
getNamespaces(SBase self)XMLNamespaces
Returns a list of the XML Namespaces declared on this SBML document.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
None
in certain very usual circumstances where a namespace is not set.
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Python method signature(s):
getNotes(SBase self)XMLNode getNotes(SBase self)
XMLNode
Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().
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Python method signature(s):
getNotesString(SBase self)string getNotesString(SBase self)
string
Returns the content of the 'notes' subelement of this object as a string.
The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.
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Python method signature(s):
getNumPlugins(SBase self)long
Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.
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Python method signature(s):
getPackageName(CompBase self)string
Returns the package name of this plugin object.
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{comp}
comp A convenience subclass of “comp” package SBase-derived classesThe CompBase class derives from SBase, and defines a few functions and features common to all SBase-derived classes in the SBML Level 3 Hierarchical Model Composition package (“comp”). Python method signature(s):
getPackageURI(CompBase self)string
Returns the XML namespace (URI) of the package extension of this object.
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Python method signature(s):
getPackageVersion(CompBase self)long
Returns the package version of the package extension of this plugin object.
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Python method signature(s):
getParentSBMLObject(SBase self)SBase getParentSBMLObject(SBase self)
SBase
Returns the parent SBML object containing this object.
This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.
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Python method signature(s):
getPlugin(SBase self, string package)SBasePlugin getPlugin(SBase self, string package)
SBasePlugin getPlugin(SBase self, long n)
SBasePlugin getPlugin(SBase self, long n)
SBasePlugin
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getPlugin(long n)
Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.
n | the index of the plug-in to return |
getPlugin(string package)
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.
package | the name or URI of the package |
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Python method signature(s):
getPrefix(SBase self)string
Returns the namespace prefix of this element.
def libsbml.ExternalModelDefinition.getReferencedModel | ( | self | ) |
Python method signature(s):
getReferencedModel(ExternalModelDefinition self)Model
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Python method signature(s):
getResourceBiologicalQualifier(SBase self, string resource)long
Returns the MIRIAM biological qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_
in the interface class libsbml.
This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose name begins with BQB_
from the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQB_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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Python method signature(s):
getResourceModelQualifier(SBase self, string resource)long
Returns the MIRIAM model qualifier associated with the given resource.
In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQM_
in the interface class libsbml.
This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource
. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose name begins with BQM_
from the interface class libsbml.
resource | string representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892' . |
BQM_
constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
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Python method signature(s):
getSBMLDocument(SBase self)SBMLDocument getSBMLDocument(SBase self)
SBMLDocument
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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Python method signature(s):
getSBOTerm(SBase self)int
Returns the integer portion of the value of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
-1
if the value is not set.
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Python method signature(s):
getSBOTermAsURL(SBase self)string
Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.
This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
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Python method signature(s):
getSBOTermID(SBase self)string
Returns the string representation of the 'sboTerm' attribute of this object.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
def libsbml.ExternalModelDefinition.getSource | ( | self | ) |
Python method signature(s):
getSource(ExternalModelDefinition self)string
Returns the value of the 'source' attribute of this ExternalModelDefinition.
def libsbml.ExternalModelDefinition.getTypeCode | ( | self | ) |
Python method signature(s):
getTypeCode(ExternalModelDefinition self)int
Returns the libSBML type code of this object instance.
SBML_
”. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName()
method on the object.
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inherited |
Python method signature(s):
getURI(SBase self)string
Gets the namespace URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.
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inherited |
Python method signature(s):
getVersion(SBase self)long
Returns the Version within the SBML Level of the SBMLDocument object containing this object.
def libsbml.ExternalModelDefinition.hasRequiredAttributes | ( | self | ) |
Python method signature(s):
hasRequiredAttributes(ExternalModelDefinition self)bool
Returns true if the 'modelRef' and 'id' attributes are set, and false if not.
This method does not check to see if the referred-to model actually exists.
True
if the attributes are correctly set; False
if not.
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inherited |
Python method signature(s):
hasValidLevelVersionNamespaceCombination(SBase self)bool
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inherited |
Python method signature(s):
isPackageEnabled(SBase self, string pkgName)bool
Predicate returning True
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, false
otherwise.
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inherited |
Python method signature(s):
isPackageURIEnabled(SBase self, string pkgURI)bool
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
True
if the given package is enabled within this object, false
otherwise.
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inherited |
Python method signature(s):
isPkgEnabled(SBase self, string pkgName)bool
Predicate returning True
if the given SBML Level 3 package is enabled with this object.
The search ignores the package version.
pkgName | the name of the package |
True
if the given package is enabled within this object, false
otherwise.
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inherited |
Python method signature(s):
isPkgURIEnabled(SBase self, string pkgURI)bool
Predicate returning True
if an SBML Level 3 package with the given URI is enabled with this object.
pkgURI | the URI of the package |
True
if the given package is enabled within this object, false
otherwise.
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inherited |
Python method signature(s):
isSetAnnotation(SBase self)bool
Predicate returning True
if this object's 'annotation' subelement exists and has content.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
True
if a 'annotation' subelement exists, False
otherwise.def libsbml.ExternalModelDefinition.isSetId | ( | self | ) |
Python method signature(s):
isSetId(ExternalModelDefinition self)bool
Predicate returning True
or False
depending on whether this object's 'id' attribute has been set.
set
/unset
/isSet
methods:
The SBML specifications define certain attributes on some classes of
objects as being optional. This requires an application to be careful
about the distinction between two cases when reading a model: (1) a given
attribute has never been set to a value, and therefore should be
assumed to have the SBML-defined default value if one exists, and (2) a
given attribute has been set to a value, but the value happens to be an
empty string. The situation can be ambiguous when reading a model from a
file or data stream and then examining the data objects that libSBML
constructs as a result. LibSBML supports these distinctions by providing
methods to set, unset, and query the status of attributes that are
optional. The methods have names of the form set
Attribute(...)
,
unset
Attribute()
, and
isSet
Attribute()
, where Attribute is the the name of the optional
attribute in question.
True
if the 'id' attribute of this object has been set, False
otherwise. def libsbml.ExternalModelDefinition.isSetMd5 | ( | self | ) |
Python method signature(s):
isSetMd5(ExternalModelDefinition self)bool
Predicate returning True
or False
depending on whether this ExternalModelDefinition's 'md5' attribute has been set.
True
if this ExternalModelDefinition's 'md5' attribute has been set, otherwise False
is returned.
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inherited |
Python method signature(s):
isSetMetaId(SBase self)bool
Predicate returning True
if this object's 'metaid' attribute is set.
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.True
if the 'metaid' attribute of this SBML object is set, False
otherwise.
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inherited |
Python method signature(s):
isSetModelHistory(SBase self)bool
Predicate returning True
if this object has a ModelHistory object attached to it.
True
if the ModelHistory of this object is set, false
otherwise.def libsbml.ExternalModelDefinition.isSetModelRef | ( | self | ) |
Python method signature(s):
isSetModelRef(ExternalModelDefinition self)bool
Predicate returning True
or False
depending on whether this ExternalModelDefinition's 'modelRef' attribute has been set.
True
if this ExternalModelDefinition's 'modelRef' attribute has been set, otherwise False
is returned. def libsbml.ExternalModelDefinition.isSetName | ( | self | ) |
Python method signature(s):
isSetName(ExternalModelDefinition self)bool
Predicate returning True
or False
depending on whether this object's 'name' attribute has been set.
set
/unset
/isSet
methods:
The SBML specifications define certain attributes on some classes of
objects as being optional. This requires an application to be careful
about the distinction between two cases when reading a model: (1) a given
attribute has never been set to a value, and therefore should be
assumed to have the SBML-defined default value if one exists, and (2) a
given attribute has been set to a value, but the value happens to be an
empty string. The situation can be ambiguous when reading a model from a
file or data stream and then examining the data objects that libSBML
constructs as a result. LibSBML supports these distinctions by providing
methods to set, unset, and query the status of attributes that are
optional. The methods have names of the form set
Attribute(...)
,
unset
Attribute()
, and
isSet
Attribute()
, where Attribute is the the name of the optional
attribute in question.
True
if the 'name' attribute of this object has been set, False
otherwise.
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inherited |
Python method signature(s):
isSetNotes(SBase self)bool
Predicate returning True
if this object's 'notes' subelement exists and has content.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
True
if a 'notes' subelement exists, False
otherwise.
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inherited |
Python method signature(s):
isSetSBOTerm(SBase self)bool
Predicate returning True
if this object's 'sboTerm' attribute is set.
True
if the 'sboTerm' attribute of this SBML object is set, False
otherwise. def libsbml.ExternalModelDefinition.isSetSource | ( | self | ) |
Python method signature(s):
isSetSource(ExternalModelDefinition self)bool
Predicate returning True
or False
depending on whether this ExternalModelDefinition's 'source' attribute has been set.
True
if this ExternalModelDefinition's 'source' attribute has been set, otherwise False
is returned.
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inherited |
Python method signature(s):
matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)bool matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)
bool
Returns True
if this object's set of XML namespaces are a subset of the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
True
if this object's collection of namespaces is a subset of sb's
, False
otherwise.
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inherited |
Python method signature(s):
matchesSBMLNamespaces(SBase self, SBase sb)bool matchesSBMLNamespaces(SBase self, SBase sb)
bool
Returns True
if this object's set of XML namespaces are the same as the given object's XML namespaces.
sb | an object to compare with respect to namespaces |
True
if this object's collection of namespaces is the same as sb's
, False
otherwise.
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inherited |
Python method signature(s):
removeFromParentAndDelete(SBase self)int
Removes this object from its parent.
If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.
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inherited |
Python method signature(s):
removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="", bool removeEmpty=True)int removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="")
int removeTopLevelAnnotationElement(SBase self, string elementName)
int
Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.
elementName | a string representing the name of the top level annotation element that is to be removed |
elementURI | an optional string that is used to check both the name and URI of the top level element to be removed |
removeEmpty | if after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default). |
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inherited |
Python method signature(s):
renameMetaIdRefs(SBase self, string oldid, string newid)
Renames all the meta-identifier attributes on this element.
ID
; the SBML object attribute itself is typically named metaid
. All attributes that hold values referring to values of type ID
are of the XML data type IDREF
. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef
.This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier |
newid | the new identifier |
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inherited |
Python method signature(s):
renameSIdRefs(SBase self, string oldid, string newid)
Renames all the SIdRef
attributes on this element, including any found in MathML content (if such exists).
SId
. In SBML Level 3, an explicit data type called SIdRef
was introduced for attribute values that refer to SId
values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRef
in Level 3. These and other methods of libSBML refer to the type SIdRef
for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.This method works by looking at all attributes and (if appropriate) mathematical formulas, comparing the identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier |
newid | the new identifier |
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inherited |
Python method signature(s):
renameUnitSIdRefs(SBase self, string oldid, string newid)
Renames all the UnitSIdRef
attributes on this element.
UnitSId
. In SBML Level 3, an explicit data type called UnitSIdRef
was introduced for attribute values that refer to UnitSId
values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef
in Level 3. These and other methods of libSBML refer to the type UnitSIdRef
for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit identifiers to the value of oldid
. If any matches are found, the matching identifiers are replaced with newid
. The method does not descend into child elements.
oldid | the old identifier |
newid | the new identifier |
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inherited |
Python method signature(s):
replaceTopLevelAnnotationElement(SBase self, XMLNode annotation)int replaceTopLevelAnnotationElement(SBase self, string annotation)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
replaceTopLevelAnnotationElement(XMLNode annotation)
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name)
followed by calling appendAnnotation(annotation_with_name)
, with the exception that the placement of the annotation element remains the same.
annotation | XMLNode representing the replacement top level annotation |
replaceTopLevelAnnotationElement(string annotation)
Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name)
followed by calling appendAnnotation(annotation_with_name)
, with the exception that the placement of the annotation element remains the same.
annotation | string representing the replacement top level annotation |
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inherited |
Python method signature(s):
setAnnotation(SBase self, XMLNode annotation)int setAnnotation(SBase self, string annotation)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setAnnotation(XMLNode annotation)
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().
annotation | an XML structure that is to be used as the new content of the 'annotation' subelement of this object |
setAnnotation(string annotation)
Sets the value of the 'annotation' subelement of this SBML object.
The content of annotation
is copied, and any previous content of this object's 'annotation' subelement is deleted.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation
that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().
annotation | an XML string that is to be used as the content of the 'annotation' subelement of this object |
def libsbml.ExternalModelDefinition.setId | ( | self, | |
args | |||
) |
Python method signature(s):
setId(ExternalModelDefinition self, string id)int
Sets the value of the 'id' attribute of this ExternalModelDefinition.
This method fails if the id
is not a valid syntax for an SId.
id | the identifier to use |
def libsbml.ExternalModelDefinition.setMd5 | ( | self, | |
args | |||
) |
Python method signature(s):
setMd5(ExternalModelDefinition self, string md5)int
Sets the value of the 'md5' attribute of this ExternalModelDefinition.
|
inherited |
Python method signature(s):
setMetaId(SBase self, string metaid)int
Sets the value of the meta-identifier attribute of this object.
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.The string metaid
is copied.
metaid | the identifier string to use as the value of the 'metaid' attribute |
|
inherited |
Python method signature(s):
setModelHistory(SBase self, ModelHistory history)int
Sets the ModelHistory of this object.
The content of history
is copied, and this object's existing model history content is deleted.
history | ModelHistory of this object. |
def libsbml.ExternalModelDefinition.setModelRef | ( | self, | |
args | |||
) |
Python method signature(s):
setModelRef(ExternalModelDefinition self, string id)int
Sets the value of the 'modelRef' attribute of this ExternalModelDefinition. Fails if the id
is not a valid syntax for an SIdRef.
def libsbml.ExternalModelDefinition.setName | ( | self, | |
args | |||
) |
Python method signature(s):
setName(ExternalModelDefinition self, string name)int
Sets the value of the 'name' attribute of this ExternalModelDefinition.
The string in name
is copied.
name | the new name for the ExternalModelDefinition |
|
inherited |
Python method signature(s):
setNamespaces(SBase self, XMLNamespaces xmlns)int
Sets the namespaces relevant of this SBML object.
The content of xmlns
is copied, and this object's existing namespace content is deleted.
The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.
xmlns | the namespaces to set |
|
inherited |
Python method signature(s):
setNotes(SBase self, XMLNode notes)int setNotes(SBase self, string notes, bool addXHTMLMarkup=False)
int setNotes(SBase self, string notes)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setNotes(string notes, bool addXHTMLMarkup = false)
Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes
.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.
notes | an XML string that is to be used as the content of the 'notes' subelement of this object |
addXHTMLMarkup | a boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p> ) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup. |
setNotes(XMLNode notes)
Sets the value of the 'notes' subelement of this SBML object.
The content of notes
is copied, and any existing content of this object's 'notes' subelement is deleted.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
notes | an XML structure that is to be used as the content of the 'notes' subelement of this object |
|
inherited |
Python method signature(s):
setSBOTerm(SBase self, int value)int setSBOTerm(SBase self, string sboid)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setSBOTerm(int value)
Sets the value of the 'sboTerm' attribute.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
value | the NNNNNNN integer portion of the SBO identifier |
setSBOTerm(string &sboid)
Sets the value of the 'sboTerm' attribute by string.
Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int
, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.
SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
def libsbml.ExternalModelDefinition.setSource | ( | self, | |
args | |||
) |
Python method signature(s):
setSource(ExternalModelDefinition self, string source)int
Sets the value of the 'source' attribute of this ExternalModelDefinition.
source | the value to use for the 'source' attribute. |
|
inherited |
Python method signature(s):
toSBML(SBase self)string *
Returns a string consisting of a partial SBML corresponding to just this object.
|
inherited |
|
inherited |
Python method signature(s):
unsetAnnotation(SBase self)int
Unsets the value of the 'annotation' subelement of this SBML object.
Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.
SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.
|
inherited |
def libsbml.ExternalModelDefinition.unsetId | ( | self | ) |
Python method signature(s):
unsetId(ExternalModelDefinition self)int
Unsets the value of the 'id' attribute of this ExternalModelDefinition.
def libsbml.ExternalModelDefinition.unsetMd5 | ( | self | ) |
Python method signature(s):
unsetMd5(ExternalModelDefinition self)int
Unsets the value of the 'md5' attribute of this ExternalModelDefinition.
|
inherited |
Python method signature(s):
unsetMetaId(SBase self)int
Unsets the value of the 'metaid' attribute of this SBML object.
ID
, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID
anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID
type. Although SBML itself specifies the use of XML ID
only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID
's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID
data type; it uses ordinary character strings, which is easier for applications to support.
|
inherited |
Python method signature(s):
unsetModelHistory(SBase self)int
Unsets the ModelHistory object attached to this object.
def libsbml.ExternalModelDefinition.unsetModelRef | ( | self | ) |
Python method signature(s):
unsetModelRef(ExternalModelDefinition self)int
Unsets the value of the 'modelRef' attribute of this ExternalModelDefinition.
def libsbml.ExternalModelDefinition.unsetName | ( | self | ) |
Python method signature(s):
unsetName(ExternalModelDefinition self)int
Unsets the value of the 'name' attribute of this ExternalModelDefinition.
|
inherited |
Python method signature(s):
unsetNotes(SBase self)int
Unsets the value of the 'notes' subelement of this SBML object.
The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.
The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and 3 specifications have considerable detail about how 'notes' element content must be structured.
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inherited |
Python method signature(s):
unsetSBOTerm(SBase self)int
Unsets the value of the 'sboTerm' attribute of this SBML object.
def libsbml.ExternalModelDefinition.unsetSource | ( | self | ) |
Python method signature(s):
unsetSource(ExternalModelDefinition self)int
Unsets the value of the 'source' attribute of this ExternalModelDefinition.